Rapid and automated design of two-component protein nanomaterials using ProteinMPNN

The design of protein-protein interfaces using physics-based design methods such as Rosetta requires substantial computational resources and manual refinement by expert structural biologists. Deep learning methods promise to simplify protein-protein interface design and enable its application to a wide variety of problems by researchers from various scientific disciplines. Here, we test the ability of a deep learning method for protein sequence design, ProteinMPNN, to design two-component tetrahedral protein nanomaterials and benchmark its performance against Rosetta. ProteinMPNN had a similar success rate to Rosetta, yielding 13 new experimentally confirmed assemblies, but required orders of magnitude less computation and no manual refinement. The interfaces designed by ProteinMPNN were substantially more polar than those designed by Rosetta, which facilitated in vitro assembly of the designed nanomaterials from independently purified components. Crystal structures of several of the assemblies confirmed the accuracy of the design method at high resolution. Our results showcase the potential of deep learning-based methods to unlock the widespread application of designed protein-protein interfaces and self-assembling protein nanomaterials in biotechnology.

Blueprinting extendable nanomaterials with standardized protein blocks

A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies, in comparison, has been much more complex, largely owing to the irregular shapes of protein structures1. Here we describe extendable linear, curved and angled protein building blocks, as well as inter-block interactions, that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight 'train track' assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence-structure relationships, it has not previously been possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank three-dimensional canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to 'back of an envelope' architectural blueprints.

Accurate computational design of three-dimensional protein crystals

Protein crystallization plays a central role in structural biology. Despite this, the process of crystallization remains poorly understood and highly empirical, with crystal contacts, lattice packing arrangements and space group preferences being largely unpredictable. Programming protein crystallization through precisely engineered side-chain-side-chain interactions across protein-protein interfaces is an outstanding challenge. Here we develop a general computational approach for designing three-dimensional protein crystals with prespecified lattice architectures at atomic accuracy that hierarchically constrains the overall number of degrees of freedom of the system. We design three pairs of oligomers that can be individually purified, and upon mixing, spontaneously self-assemble into >100 µm three-dimensional crystals. The structures of these crystals are nearly identical to the computational design models, closely corresponding in both overall architecture and the specific protein-protein interactions. The dimensions of the crystal unit cell can be systematically redesigned while retaining the space group symmetry and overall architecture, and the crystals are extremely porous and highly stable. Our approach enables the computational design of protein crystals with high accuracy, and the designed protein crystals, which have both structural and assembly information encoded in their primary sequences, provide a powerful platform for biological materials engineering.

De novo design of monomeric helical bundles for pH-controlled membrane lysis

Targeted intracellular delivery via receptor-mediated endocytosis requires the delivered cargo to escape the endosome to prevent lysosomal degradation. This can in principle be achieved by membrane lysis tightly restricted to endosomal membranes upon internalization to avoid general membrane insertion and lysis. Here, we describe the design of small monomeric proteins with buried histidine containing pH-responsive hydrogen bond networks and membrane permeating amphipathic helices. Of the 30 designs that were experimentally tested, all expressed in Escherichia coli, 13 were monomeric with the expected secondary structure, and 4 designs disrupted artificial liposomes in a pH-dependent manner. Mutational analysis showed that the buried histidine hydrogen bond networks mediate pH-responsiveness and control lysis of model membranes within a very narrow range of pH (6.0-5.5) with almost no lysis occurring at neutral pH. These tightly controlled lytic monomers could help mediate endosomal escape in designed targeted delivery platforms.

Rapid and automated design of two-component protein nanomaterials using ProteinMPNN

The design of novel protein-protein interfaces using physics-based design methods such as Rosetta requires substantial computational resources and manual refinement by expert structural biologists. A new generation of deep learning methods promises to simplify protein-protein interface design and enable its application to a wide variety of problems by researchers from various scientific disciplines. Here we test the ability of a deep learning method for protein sequence design, ProteinMPNN, to design two-component tetrahedral protein nanomaterials and benchmark its performance against Rosetta. ProteinMPNN had a similar success rate to Rosetta, yielding 13 new experimentally confirmed assemblies, but required orders of magnitude less computation and no manual refinement. The interfaces designed by ProteinMPNN were substantially more polar than those designed by Rosetta, which facilitated in vitro assembly of the designed nanomaterials from independently purified components. Crystal structures of several of the assemblies confirmed the accuracy of the design method at high resolution. Our results showcase the potential of deep learning-based methods to unlock the widespread application of designed protein-protein interfaces and self-assembling protein nanomaterials in biotechnology.

Hierarchical design of pseudosymmetric protein nanoparticles

Discrete protein assemblies ranging from hundreds of kilodaltons to hundreds of megadaltons in size are a ubiquitous feature of biological systems and perform highly specialized functions1-3. Despite remarkable recent progress in accurately designing new self-assembling proteins, the size and complexity of these assemblies has been limited by a reliance on strict symmetry4,5. Inspired by the pseudosymmetry observed in bacterial microcompartments and viral capsids, we developed a hierarchical computational method for designing large pseudosymmetric self-assembling protein nanomaterials. We computationally designed pseudosymmetric heterooligomeric components and used them to create discrete, cage-like protein assemblies with icosahedral symmetry containing 240, 540, and 960 subunits. At 49, 71, and 96 nm diameter, these nanoparticles are the largest bounded computationally designed protein assemblies generated to date. More broadly, by moving beyond strict symmetry, our work represents an important step towards the accurate design of arbitrary self-assembling nanoscale protein objects.

Hierarchical design of pseudosymmetric protein nanoparticles

Discrete protein assemblies ranging from hundreds of kilodaltons to hundreds of megadaltons in size are a ubiquitous feature of biological systems and perform highly specialized functions 1-3. Despite remarkable recent progress in accurately designing new self-assembling proteins, the size and complexity of these assemblies has been limited by a reliance on strict symmetry 4,5. Inspired by the pseudosymmetry observed in bacterial microcompartments and viral capsids, we developed a hierarchical computational method for designing large pseudosymmetric self-assembling protein nanomaterials. We computationally designed pseudosymmetric heterooligomeric components and used them to create discrete, cage-like protein assemblies with icosahedral symmetry containing 240, 540, and 960 subunits. At 49, 71, and 96 nm diameter, these nanoparticles are the largest bounded computationally designed protein assemblies generated to date. More broadly, by moving beyond strict symmetry, our work represents an important step towards the accurate design of arbitrary self-assembling nanoscale protein objects.

Blueprinting expandable nanomaterials with standardized protein building blocks

A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies in comparison has been much more complex, largely due to the irregular shapes of protein structures 1 . Here we describe extendable linear, curved, and angled protein building blocks, as well as inter-block interactions that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight "train track" assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence-structure relationships, it has not been previously possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank 3D canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to "back of an envelope" architectural blueprints.

Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock

Computationally designed multi-subunit assemblies have shown considerable promise for a variety of applications, including a new generation of potent vaccines. One of the major routes to such materials is rigid body sequence-independent docking of cyclic oligomers into architectures with point group or lattice symmetries. Current methods for docking and designing such assemblies are tailored to specific classes of symmetry and are difficult to modify for novel applications. Here we describe RPXDock, a fast, flexible, and modular software package for sequence-independent rigid-body protein docking across a wide range of symmetric architectures that is easily customizable for further development. RPXDock uses an efficient hierarchical search and a residue-pair transform (RPX) scoring method to rapidly search through multidimensional docking space. We describe the structure of the software, provide practical guidelines for its use, and describe the available functionalities including a variety of score functions and filtering tools that can be used to guide and refine docking results towards desired configurations.

Computational design of non-porous, pH-responsive antibody nanoparticles

Programming protein nanomaterials to respond to changes in environmental conditions is a current challenge for protein design and important for targeted delivery of biologics. We describe the design of octahedral non-porous nanoparticles with the three symmetry axes (four-fold, three-fold, and two-fold) occupied by three distinct protein homooligomers: a de novo designed tetramer, an antibody of interest, and a designed trimer programmed to disassemble below a tunable pH transition point. The nanoparticles assemble cooperatively from independently purified components, and a cryo-EM density map reveals that the structure is very close to the computational design model. The designed nanoparticles can package a variety of molecular payloads, are endocytosed following antibody-mediated targeting of cell surface receptors, and undergo tunable pH-dependent disassembly at pH values ranging between to 5.9-6.7. To our knowledge, these are the first designed nanoparticles with more than two structural components and with finely tunable environmental sensitivity, and they provide new routes to antibody-directed targeted delivery.

A microwave applicator for uniform irradiation by circularly polarized waves in an anechoic chamber

Microwave applicators are widely employed for materials heating in scientific research and industrial applications, such as food processing, wood drying, ceramic sintering, chemical synthesis, waste treatment, and insect control. For the majority of microwave applicators, materials are heated in the standing waves of a resonant cavity, which can be highly efficient in energy consumption, but often lacks the field uniformity and controllability required for a scientific study. Here, we report a microwave applicator for rapid heating of small samples by highly uniform irradiation. It features an anechoic chamber, a 24-GHz microwave source, and a linear-to-circular polarization converter. With a rather low energy efficiency, such an applicator functions mainly as a research tool. This paper discusses the significance of its special features and describes the structure, in situ diagnostic tools, calculated and measured field patterns, and a preliminary heating test of the overall system.

Signal-dependent fra-2 regulation in skeletal muscle reserve and satellite cells

Activator protein-1 (AP-1) is a ubiquitous transcription factor that paradoxically also has some tissue-specific functions. In skeletal muscle cells, we document that the AP-1 subunit, Fra-2, is expressed in the resident stem cells (Pax7-positive satellite cells) and also in the analogous undifferentiated ‘reserve' cell population in myogenic cultures, but not in differentiated myofiber nuclei. Silencing of Fra-2 expression enhances the expression of differentiation markers such as muscle creatine kinase and myosin heavy chain, indicating a possible role of Fra-2 in undifferentiated myogenic progenitor cells. We observed that Fra-2 is a target of cytokine-mediated extracellular signal-regulated kinase-1/2 signaling in cultured muscle cells, and extensive mass spectrometry and mutational analysis identified S320 and T322 as regulators of Fra-2 protein stability. Interestingly, Fra-2 S320 phosphorylation occurs transiently in activated satellite cells and is extinguished in myogenin-positive differentiating cells. Thus, cytokine-mediated Fra-2 expression and stabilization is linked to regulation of myogenic progenitor cells having implications for the molecular regulation of adult muscle stem cells and skeletal muscle regeneration.

Abnormal foraging behavior induced by sublethal dosage of imidacloprid in the honey bee (Hymenoptera: Apidae)

Although sublethal dosages of insecticide to nontarget insects have never been an important issue, they are attracting more and more attention lately. It has been demonstrated that low dosages of the neonicotinoid insecticide imidacloprid may affect honey bee, Apis mellifera L., behavior. In this article, the foraging behavior of the honey bee workers was investigated to show the effects of imidacloprid. By measuring the time interval between two visits at the same feeding site, we found that the normal foraging interval of honey bee workers was within 300 s. However, these honey bee workers delayed their return visit for > 300 s when they were treated orally with sugar water containing imidacloprid. This time delay in their return visit is concentration-dependent, and the lowest effective concentration was found to be 50 microg/liter. When bees were treated with an imidacloprid concentration higher than 1,200 microg/liter, they showed abnormalities in revisiting the feeding site. Some of them went missing, and some were present again at the feeding site the next day. Returning bees also showed delay in their return trips. Our results demonstrated that sublethal dosages of imidacloprid were able to affect foraging behavior of honey bees.

Quantum superposition of high spin states in the single molecule magnet Ni4

Quantum tunneling of the magnetization in a single molecule magnet has been studied in experiments that combine microwave spectroscopy with high sensitivity magnetic measurements. By monitoring spin-state populations in the presence of microwave radiation, the energy splittings between low lying superpositions of high-spin states of single molecule magnet Ni4 (S=4) have been measured. Absorption linewidths give an upper bound on the rate of decoherence. Pulsed microwave experiments provide a measure of energy relaxation time, which is found to increase with frequency.

Retinal regionalization and heterogeneity of butterfly eyes

The regional characteristics of the eyes of butterflies from different families have been surveyed using epi-illumination microscopy, utilizing the eyeshine visible due to the tapetum situated proximally to the rhabdom. All butterflies studied have a high spatial acuity in the frontal region. The facet diameter varies slightly across the eye, and the interommatidial angle and the eye parameter p are especially large dorsally. Whereas the ommatidial lattice is generally highly regular, the eyeshine colours distinctly depend on the species. Sometimes the eyeshine is locally uniform, but often it is heterogeneous. It is hypothesized that the regional characteristics as well as the local heterogeneity are adaptations that optimize spectral discrimination.

Initial treatment of traumatic hip dislocations in the adult

The initial treatment of traumatic hip dislocations is critical to successful treatment of this injury. It generally is agreed that prompt reduction with the patient under anesthesia or sedation is required. Delay in reduction of posterior hip dislocations is associated with avascular necrosis of the hip. Occasionally the hip dislocation will be irreducible. Various methods to reduce hip dislocations have been described in the literature. The superiority of one particular technique has not been shown and the choice of reduction maneuver must be tailored to the condition of the patient. Traumatic hip dislocations often are associated with multiple injuries that may limit the options available for initial treatment of the hip dislocation. Adherence to general principles of skeletal reduction will increase the ease of reduction and decrease the risk of iatrogenic injury during reduction. Additional clinical and radiographic evaluation of the hip that was reduced often is necessary to determine whether subsequent open treatment is required.

Glycosylation of fluoroquinolones through direct and oxygenated polymethylene linkages as a sugar-mediated active transport system for antimicrobials

We report herein the synthesis and biological testing of several glycosylated derivatives of some fluoroquinolone antibiotics. In particular, we have prepared several glycosylated derivatives of ciprofloxacin (2) in which the carbohydrate units are linked to the free secondary amine of the piperazine unit by: (a) no linker (e.g., a glycosylamine), (b) a beta-oxyethyl linker, and (c) a gamma-oxypropyl linker. Both glucose and galactose were used as carbohydrates so that six compounds of this type were prepared, e.g., no linker 4a,b, oxyethyl linker 5a,b, and oxypropyl linker 6a,b. In addition the aryl glycosides of glucose and galactose (7a,b) were prepared from the active 1-(4-hydroxyphenyl)fluoroquinolone (3.) The syntheses of the glycosylamines 4a,b involved the direct condensation of glucose and galactose with the hydrochloride salt of ciprofloxacin (2). For the oxyalkyl-linked compounds, we first prepared the peracetylated omega-bromoalkyl glycopyranosides 14a,b and 15a,b and then coupled them to the allyl ester of ciprofloxacin (11) to give, after saponification to remove all of the esters, the desired fluoroquinolone carbohydrates 5a,b and 6a,b. The final series was prepared from 2,4,5-trifluorobenzoyl chloride (22) which gave 3 in four precedented steps. Coupling of 3 with the peracetylated glucosyl and galactosyl halides 12a,b and 26 afforded, after saponification, the desired aryl glycosides 7a,b. Six of these derivatives of ciprofloxacin-4a,b, 5a,b, and 6a,b-were subjected to microbiological screening. Of the six, compound 6a showed the highest activity. Since 6a would give the hydroxypropyl-substituted ciprofloxacin on hydrolysis and its activity is approximately 4-8 times less than that of ciprofloxacin (2), this implies that compound 6a is probably being actively transported. Thus preliminary results suggest that some of the compounds are stable in culture conditions and may be differentially transported by multiple resistant organisms. In some cases, the addition of a linker and a carbohydrate to ciprofloxacin lessens, but does not eliminate, antimicrobial activity.

Treatment of type II and type III open tibia fractures in children

OBJECTIVES

To determine whether severe open tibial fractures in children behave like similar fractures in adults.

DESIGN AND SETTING

A combined retrospective and prospective review evaluated treatment protocol for type II and type III open tibial fractures in children over a ten-year period from 1984 to 1993.

PATIENTS

Twenty-three fractures were studied in children aged 3.5 to 14.5 (18 boys and 5 girls). There were six type II, eight type IIIA, and nine type IIIB fractures. Type I fractures were not included. Seven fractures were comminuted with significant butterfly fragments or segmental patterns.

INTERVENTION

Treatment consisted of adequate debridement of soft tissues, closure of dead space, and stabilization with external fixation. Bone debridement only included contaminated devitalized bone or devitalized bone without soft tissue coverage. Bone that could be covered despite periosteal stripping was preserved.

MAIN OUTCOME MEASUREMENTS

Clinical and roentgenographic examinations were used to determine time to union.

RESULTS

All fractures in this series healed between eight and twenty-six weeks. Wound coverage included two flaps, three skin grafts, and two delayed primary closures. No bone grafts were required. There were no deep infections, growth arrests, or malunions. Follow-up has ranged from six months to four years.

CONCLUSIONS

Open tibia fractures in children differ from similar fractures in adults in the following ways: soft tissues have excellent healing capacity, devitalized bone that is not contaminated or exposed can be saved and will become incorporated, and external fixation can be maintained until the fracture has healed. Periosteum in young children can form bone even in the face of bone loss.

The use of an anterior incision of the meniscus for exposure of tibial plateau fractures requiring open reduction and internal fixation

The purpose of this study was to examine the use of an anterior incision of the meniscus for exposure of tibial plateau fractures. We studied 27 fractures of the proximal tibia treated with open reduction and internal fixation (ORIF). There were nine unicondylar fractures (five A-O B2; four A-O B3) fixed with plates and screws and 18 bicondylar fractures (seven A-O C1; five A-O C2; six A-O C3) fixed with combination internal and external fixation. Length of follow-up averaged 26 months. All patients were treated with an anterior incision of the meniscus and retraction with the condyle. Of the 18 bicondylar fractures, nine severely displaced fractures were found to have peripherally detached menisci. Unicondylar fractures did not display this finding. After fixation, menisci were repaired at the periphery and sewn to the original anterior insertion. The repair begins posteriorly and advances the cartilage to ensure anatomic placement. There were four medial and 23 lateral menisci in this series. Ten patients underwent knee arthroscopy 6 months to 2 years post-ORIF as a routine procedure during hardware removal. All menisci were found to be healed to the periphery and were stable. There were no gross tears. In one patient, the anterior meniscal incision could be visualized. No patients developed mechanical symptoms either in postoperative rehabilitation or postoperative follow-up at a maximum of 6 years. All patients had > 125 degrees of motion. Less motion when compared with the normal knee was felt to be related to more complex fracture patterns. In conclusion, the anterior meniscal incision allows for excellent exposure of severe proximal tibia fractures. This technique allows for anatomic meniscal repair and early rehabilitation. Arthroscopic examination confirms peripheral meniscal healing. No patient experienced clinical symptoms of meniscal pathology.

Metaphyseal dissociation fractures of the proximal tibia. An analysis of treatment and complications

A study was done of 44 metaphyseal dissociation fractures of the proximal tibia in 42 patients (27 men and 15 women, aged 22 to 77 years; mean, 42 years). Follow-up ranged from 6 months to 4 years. There were 2 study groups: a retrospective group (group 1, 22 fractures) given a variety of treatments ranging from casts to dual plates, and a prospective group (group 2, 22 fractures) treated by combining external fixation and optional minimal internal fixation. There were 12 comminuted fractures in group 1 and 20 in group 2 (P < 0.01). All fractures eventually healed, with an average healing time in group 1 of 3.8 months, and 5.3 months in group 2. There was one delayed union in group 2. Results were graded from poor to excellent, based on pain, range-of-motion, and malunion. There were 6 poor and 4 fair results in group 1, and no poor and 3 fair results in group 2. Complications included 6 deep infections, 5 in group 1 (1 requiring a free-flap procedure); and 1 pin-tract infection resulting in septic arthritis in group 2. There were 7 gastrocnemius flaps required in group 1, and 1 in group 2. The results of this study suggest that patients treated with external fixation had better results with less infection and soft-tissue complications than those treated with conventional internal fixation.

Gunshot wounds to the forearm

The rising incidence of civilian gunshot wounds has been well documented. Approximately 4% to 20% of these wounds consist of injuries to the forearm. An organized approach to the treatment of these injuries should be used to obtain an optimal result. Factors to be considered in treatment include the type of weapon and bullet involved, the neurovascular status of the patient, the possibility of compartment syndrome, the presence and type of fracture, and soft-tissue injury.

Timing of internal fixation in low-velocity extremity gunshot fractures

A ten-year retrospective review of extremity long bone gunshot fractures treated operatively at the Elmhurst City Hospital Center, New York, was performed to examine the operative outcomes with regard to immediate, intermediate, and delayed fixation. A total of 121 low-velocity gunshot fractures were evaluated in 107 patients. Cases were separated into three groups according to the actual timing of the internal fixation procedure. The results revealed a total deep infection rate of 2.6% (3/121) and a nonunion rate of 3.3% (4/121), with no significant differences among the three groups. Early internal fixation reduced comparative hospital stay length and overall costs for operative patients.

Inserting distal screws into interlocking IM nails

The use of interlocking IM nails is commonplace in major trauma centers. Currently, an accurate guide for inserting the distal screws is not available. Most centers use the "free-hand" technique. Every surgeon must be familiar with this method to insert the screws. We describe our protocol for inserting the distal screws into interlocking IM nails.

Pseudomonas aeruginosa as a causative agent of cervical osteomyelitis. Case report and review of the literature

Pseudomonas aeruginosa osteomyelitis and epidural abscess of the cervical spine developed in a previously healthy, 73-year-old man who was not an intravenous drug abuser. In the recent literature, Pseudomonas cervical osteomyelitis has been reported only in intravenous drug abusers or in otherwise healthy individuals after a tooth extraction. In the literature of the past 30 years, isolated cases of cervical osteomyelitis were associated with urinary tract infections. The majority of these cases involved urinary tract instrumentation. The pathogenesis remains controversial. It appears that spontaneous cervical osteomyelitis in a non-intravenous drug abuser has not been previously reported.